There are two different methods I use for printing different filaments based on height for 3D design
The simpler, but cruder method is to use the ‘Pause at zpos’ option on the flashforge menu to stop the print at the desired level, and then swap the filament while the machine is paused (I’ve done this a few times. Provided you’ve got the printer’s ‘Pause with heat’ option enabled, you shouldn’t have any problems with it. Though since the printer doesn’t wipe the nozzle after resuming from pause, there might be a little oozing that catches on where it re-starts)
The other option, for if you’re confident doing a dual extrusion print, is to add a second process in Simplify3D, set it to use the extruder that is loaded with the secondary filament, and then set the ‘Start/stop printing at height’ options in the ‘Advanced’ tab in both processes to set where you want one to finish up and the other to begin.